From augmented microscopy to the topological transformer: a new approach in cell image analysis for Alzheimer's research

Cell image analysis is crucial in Alzheimer's research to detect the presence of A$\beta$ protein inhibiting cell function. Deep learning speeds up the process by making only low-level data sufficient for fruitful inspection. We first found Unet is most suitable in augmented microscopy by comparing performance in multi-class semantics segmentation. We develop the augmented microscopy method to capture nuclei in a brightfield image and the transformer using Unet model to convert an input image into a sequence of topological information. The performance regarding Intersection-over-Union is consistent concerning the choice of image preprocessing and ground-truth generation. Training model with data of a specific cell type demonstrates transfer learning applies to some extent. The topological transformer aims to extract persistence silhouettes or landscape signatures containing geometric information of a given image of cells. This feature extraction facilitates studying an image as a collection of one-dimensional data, substantially reducing computational costs. Using the transformer, we attempt grouping cell images by their cell type relying solely on topological features. Performances of the transformers followed by SVM, XGBoost, LGBM, and simple convolutional neural network classifiers are inferior to the conventional image classification. However, since this research initiates a new perspective in biomedical research by combining deep learning and topology for image analysis, we speculate follow-up investigation will reinforce our genuine regime.